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author bjoern-gruening
date Thu, 15 Mar 2012 05:23:03 -0400
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1 <tool id="multi_antiSMASH" name="Secondary Metabolites" version="0.1">
2 <description>and Antibiotics Analysis (multi antiSMASH)</description>
3 <command interpreter="python">multi_antiSMASH_wrapper.py
4 ## The command is a Cheetah template which allows some Python based syntax.
5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
6 ## ./antismash.py Tue6071_genome.fasta --geneclustertypes 1 --fullblast y --fullhmm y
7
8 #if $input_opts.input_opts_selector == "fasta":
9 --input $infile
10 --glimmer_prediction $glimmer_prediction
11 #else:
12 --input $infile
13 #end if
14
15 --input_format $input_opts.input_opts_selector
16
17 $eukaryotic
18 $genecluster
19 $smCOG
20 $wg_blast
21 --geneclustertypes $geneclustertypes
22 --geneclusterprots $geneclusterprots
23 --geneclusterprots_gff $geneclusterprots_gff
24 --embl_path $embl
25 > /dev/null 2> /dev/null
26 </command>
27 <inputs>
28
29 <conditional name="input_opts">
30 <param name="input_opts_selector" type="select" label="Input format">
31 <option value="fasta" selected="True">FASTA file (not annotated)</option>
32 <option value="genbank">GenBank file (annotated)</option>
33 <option value="embl">embl file (annotated)</option>
34 </param>
35 <when value="fasta">
36 <param name="infile" type="data" format="fasta" label="Sequence File"/>
37 <param name="glimmer_prediction" type="data" format="tabular" label="Glimmer Prediction File"/>
38 </when>
39 <when value="embl">
40 <param name="infile" type="data" format="embl" label="embl Sequence File"/>
41 </when>
42 <when value="genbank">
43 <param name="infile" type="data" format="embl" label="GenBank Sequence File"/>
44 </when>
45 </conditional>
46
47
48
49
50 <param name="eukaryotic" type="boolean" label="is the DNA of Eukaryotic origin" truevalue="--eukaryotic" falsevalue="" checked="false" />
51 <param name="smCOG" type="boolean" label="smCOG analysis for functional prediction and phylogenetic analysis of genes" falsevalue="" truevalue="--smcogs" checked="true" />
52 <param name="genecluster" type="boolean" label="Gene Cluster Blast Comparative Analysis" truevalue="--clusterblast" falsevalue="" checked="true" />
53 <param name="wg_blast" type="boolean" label="Whole genome BLAST results in EMBL output" truevalue="--fullblast" falsevalue="" checked="true" />
54 <param name="pfam" type="boolean" label="Whole genome PFAM results in EMBL output" truevalue="--fullhmm" falsevalue="" checked="true" />
55
56 <param name="geneclustertypes" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
57 <option value="1" selected="True">all</option>
58 <option value="2">type I polyketide synthases</option>
59 <option value="3">type II polyketide synthases</option>
60 <option value="4">type III polyketide synthases</option>
61 <option value="5">nonribosomal peptide synthetases</option>
62 <option value="6">terpene synthases</option>
63 <option value="7">lantibiotics</option>
64 <option value="8">bacteriocins</option>
65 <option value="9">beta-lactams</option>
66 <option value="10">aminoglycosides / aminocyclitols</option>
67 <option value="11">aminocoumarins</option>
68 <option value="12">siderophores</option>
69 <option value="13">ectoines</option>
70 <option value="14">butyrolactones</option>
71 <option value="15">indoles</option>
72 <option value="16">nucleosides</option>
73 <option value="17">phosphoglycolipids</option>
74 <option value="18">melanins</option>
75 <option value="19">others</option>
76 </param>
77 </inputs>
78 <outputs>
79 <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
80 <data format="gff3" name="geneclusterprots_gff" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
81 <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
82 </data>
83 </outputs>
84 <help>
85
86 .. class:: infomark
87
88 That version of antiSMASH can only handle multiple sequence files.
89 It will run antiSMASH automatically on each sequence and aggregate the most important information from all runs.
90 It will not provide an interactive HTML output file. If you need that please use the normal antiSMASH version on a single sequence.
91
92
93 .. class:: warningmark
94
95 **Warning on FASTA Header**
96
97 The FASTA header should not contain any special letters, like '|'. Please replace them with the 'sed-tool'.
98
99
100 **What it does**
101
102 antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
103 It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
104
105
106 **Input**
107
108 If you don't have an annotated GenBank or embl file you also can provide a glimmer prediction output. Created with glimmer or glimmerHMM.
109
110
111 **References**
112
113 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
114 Rainer Breitling and Eriko Takano (2011). antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research, doi: 10.1093/nar/gkr466.
115
116 http://antismash.secondarymetabolites.org/help.html
117
118 </help>
119 </tool>